After his ordeal with Udo Jin-e, Himura Kenshin's brief period of peace is interrupted by the presence of Hajime Saito, the former captain of the Shinsengumi who assumed an alias in Tokyo's police force. With Takani Megumi's freedom at the balance, Kenshin learns that he is being enlisted in a covert operation at the city of Kyoto. There, Kenshin deals with a small army under the leadership of Hitokiri Battōsai replacement and successor, who was deemed a great enough threat to the Meiji government's stability that they attempted to burn him alive: Makoto Shishio.